Hello:
I am trying to use pymol to view the pes for an RNA-Protein complex.
But, I want to use two different dx maps: one for RNA and one for the
protein.
Here is what I did:
1) I read into pymol the pdb file for the entire RNA-protein complex. It
looks good.
2) I then read in a protein.dx map hoping that it would overlap with the
protein segment. It didn't work.
Can someone please help me with this?
The reason for the two pes maps is that the RNA and protein have different
characteristics, and I want to manipulate them separately.
Thanks for all your help in advance.
Kind regards,
Angelo

Hi--
Can the roving mesh be used without changing the model appearance?
I'd prefer to just show the entire structure as lines only, but it
looks like the roving_detail setting controls both model and mesh.
thanks,
Nat

In a Python script I am working on I would like to get a list of the
scenes that are defined. Unfortunately, cmd.scene('*') just prints the
list to stdout, but doesn't return anything. That is, if I have a
script test.py that looks like
> from pymol import cmd
> x = cmd.scene('*')
> print x
And I type "run test.py" in PyMol I get the following output
> PyMOL>run test.py
> scene: stored scenes:
> F1 F2
> x='None'
Is there a different mechanism to get a list of defined scenes? Or an
argument, I've missed?
I have the following work around
> from pymol import cmd
> import sys
> from StringIO import StringIO
>
> tmp = StringIO()
> (tmp,sys.stdout) = (sys.stdout,tmp)
> cmd.scene('*')
> (tmp,sys.stdout) = (sys.stdout,tmp)
> list = tmp.getvalue().split("\n")[1].split()
> print list
which generates what I want
> PyMOL>run test.py
> ['F1', 'F2']
but that seems less than elegant.
Malcolm

Hi Annalisa,
Is the original coordinate file an NMR structure? It looks to me like
there are several copies of each atom, which is consistent with the pdb
file resulting from an NMR refinement. These will usually have several
different models of the peptide, all consistent with the NMR data.
You will need to extract just one set of coordinates and look at those.
Which set of coordinates to use depends on the software used to generate
the pdb, but look for the first or the 'best' model, the pdb header
should tell you which is best.
Hope this helps at bit
Andrew Purkiss-Trew
On Thu, 2008-12-18 at 15:40 +0100, annalisa bordogna wrote:
> Hi all,
> I have a little problem with the visualization of a peptide
> conformation: as you can see from the picture I enclose, the structure
> appears as if every atom is bound to every neighbour atom. What (and
> how) can I set in PyMOL, to visualize a correct structure?
>
> Thank you very much for your help.
> Best regards,
> Annalisa
>
> -------------------------------------------------------
> Annalisa Bordogna
> Ph.D. Student
> Università degli Studi di Milano - Bicocca
> Milano, IT
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
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Hi Andrew,
thank you for your answer: now I have a clue!
I knew that the structure is a NMR model, but what I didn't understand was
that some atoms were repeated (with different coordinates). Now I have
pruned my structure file and I can see a much more acceptable structure.
Thank you very much,
Annalisa
2008/12/19 Andrew Purkiss-Trew <a.purkiss@...>
> Hi Annalisa,
>
> Is the original coordinate file an NMR structure? It looks to me like
> there are several copies of each atom, which is consistent with the pdb
> file resulting from an NMR refinement. These will usually have several
> different models of the peptide, all consistent with the NMR data.
>
> You will need to extract just one set of coordinates and look at those.
> Which set of coordinates to use depends on the software used to generate
> the pdb, but look for the first or the 'best' model, the pdb header
> should tell you which is best.
>
> Hope this helps at bit
>
> Andrew Purkiss-Trew
>
> On Thu, 2008-12-18 at 15:40 +0100, annalisa bordogna wrote:
> > Hi all,
> > I have a little problem with the visualization of a peptide
> > conformation: as you can see from the picture I enclose, the structure
> > appears as if every atom is bound to every neighbour atom. What (and
> > how) can I set in PyMOL, to visualize a correct structure?
> >
> > Thank you very much for your help.
> > Best regards,
> > Annalisa
> >
> > -------------------------------------------------------
> > Annalisa Bordogna
> > Ph.D. Student
> > Università degli Studi di Milano - Bicocca
> > Milano, IT
> >
> ------------------------------------------------------------------------------
> > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,
> Nevada.
> > The future of the web can't happen without you. Join us at MIX09 to help
> > pave the way to the Next Web now. Learn more and register at
> >
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> > _______________________________________________ PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

Mark,
PyMOL does not have such abilities at present.
Can such concepts even be defined in a precise, objective, and unambiguous
fashion?
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:support@...
> -----Original Message-----
> From: Mark Collins [mailto:mnc2003@...]
> Sent: Thursday, December 18, 2008 7:38 AM
> To: pymol-users@...
> Subject: [PyMOL] surface properties
>
> Hi All
> I have searched thru the archive and couldn't find an answer,
> to this. I would like to make pymol surface(s) colored by
> (1) hydrophobicity and (2) concavity/convexity.
> These are easily produced in grasp, so one possibility maybe
> to import some type of grasp file.
> Thanks in advance for suggestions, websites, or tutorials, etc.
> Mark
>
> --------------------------------------------------------------
> ----------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las
> Vegas, Nevada.
> The future of the web can't happen without you. Join us at
> MIX09 to help pave the way to the Next Web now. Learn more
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> _______________________________________________
> PyMOL-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/pymol-users

Annalisa,
If bonds are not explicitly provided in the input file, then PyMOL infers
bonding based on distance. Are the input coordinates valid? It looks like
the atoms may be too close together in space...
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:support@...
_____
From: annalisa bordogna [mailto:annalisa.bordogna@...]
Sent: Thursday, December 18, 2008 6:40 AM
To: pymol-users@...
Subject: [PyMOL] weird visualization of a peptide structure
Hi all,
I have a little problem with the visualization of a peptide conformation: as
you can see from the picture I enclose, the structure appears as if every
atom is bound to every neighbour atom. What (and how) can I set in PyMOL, to
visualize a correct structure?
Thank you very much for your help.
Best regards,
Annalisa
-------------------------------------------------------
Annalisa Bordogna
Ph.D. Student
Università degli Studi di Milano - Bicocca
Milano, IT

Dear All,
Thanks for all your suggestions on ray tracing the protein gallery.
In the end, I used several of the techniques suggested, and everything
worked out really well!
To summarize:
1. Use the grid_mode option (only available in the compiled from
source pymols)
2. Make a fake .pdb that has the corners and centers of a 3D box to
use for alignment
3. Use the set_view command to apply the same viewing matrix
4. Use the zoom command with a center and a distance specified.
Also, the cealign package is really helpful for aligning and
translating very dissimilar molecules.
Thanks! and all the best,
--Buz
On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote:
> Hi Buz,
>
> You can use "center" as a selection name for input with zoom, along
> with a
> distance value.
>
> zoom center, distance
>
> e.g.
>
> # first, get the object you want in the center of the screen
>
> orient
>
> # then zoom the viewer by a fixed amount about the center point
>
> zoom center, 10
>
> # you may also wish to move the clipping planes in/out to avoid
> cutting into
> any of the molecular representations:
>
> clip atoms, 4, selection=all
>
> # also, depending upon the application, you might want to disable
> perspective
>
> set orthoscopic
>
> # get rid of background pixels
>
> unset opaque_background
>
> # render
>
> ray
>
> # and save
>
> save struct001.png
>
> Cheers,
> Warren
>
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:support@...
>
>
>
>> -----Original Message-----
>> From: Buz Barstow [mailto:buzb@...]
>> Sent: Monday, December 15, 2008 11:42 AM
>> To: pymol-users@...
>> Subject: [PyMOL] Ray Tracing A Protein Gallery
>>
>> Dear All,
>>
>> I'm making a gallery of protein molecules for my PhD thesis.
>> I'd like to find an automatic way to ensure that all of the
>> ray traced images have the same scale. Is there an easy way
>> to do this?
>>
>> Thanks! and all the best,
>>
>> --Buz
>>
>> --------------------------------------------------------------
>> ----------------
>> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las
>> Vegas, Nevada.
>> The future of the web can't happen without you. Join us at
>> MIX09 to help pave the way to the Next Web now. Learn more
>> and register at
>> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
> .visitmix.com/
>> _______________________________________________
>> PyMOL-users mailing list
>> PyMOL-users@...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas,
> Nevada.
> The future of the web can't happen without you. Join us at MIX09 to
> help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Dear All,
I'd like to mutate an ion in pymol from a potassium to a sodium. Is
there an easy way to do this from the command line without having to
edit the pdb file of the structure?
Also, when one displays an atom (for instance a K atom) using the
spheres representation, is the radius of the sphere equal to the
Pauling radius of the atom (under the assumption that it is ionized)?
For K, it looks like it is.
Thanks! and all the best,
--Buz

Hi All
I have searched thru the archive and couldn't find an answer, to this. I
would like to make pymol surface(s) colored by (1) hydrophobicity and (2)
concavity/convexity.
These are easily produced in grasp, so one possibility maybe to import
some type of grasp file.
Thanks in advance for suggestions, websites, or tutorials, etc.
Mark

Is it possible to add additional python modules to a MacPyMOL installation?
I am trying to install the PyNMR plugin:
http://maple.rsvs.ulaval.ca/mediawiki/index.php/PyNMR
And it requires the Numeric python module. I have an external python
installation built with the module, but it seems that MacPyMOL uses a
bundled python interpreter.
I tried setting the PYTHONPATH to the modules directory of my python
build, but I get errors like this:
/programs/i386-mac/python/2.5.2/lib/python2.5/site-packages/Numeric/Numeric.py:91: RuntimeWarning: Python C API version mismatch for module multiarray: This Python has API version 1012, module multiarray has version 1013.
I poked around in the PyMOLX11Hybrid.app directories, but didn't see an
obvious place I could add a module installation.
Thanks.
-ben
--
Ben Eisenbraun
Structural Biology Grid Harvard Medical School
http://sbgrid.orghttp://hms.harvard.edu

Hello,
When I try to add a surface to a very large structure and PyMol gives me the error message "PyMol just ran out of memory and crashed...." am I receiving this message due to limitations of the PyMol program, or do I need to install more memory on my computer?
Thanks
-Crystal

Mark,
Sorry, but the current C code appears to be broken. For future reference,
you should be able to do the following:
load $TUT/1hpv.pdb
# absolute linear scaling from the B factor
set cartoon_putty_transform, 7
# set a base radius of 1.0 (will be scaled based on B factors)
set cartoon_putty_radius, 1.0
# no limits on the scaling
set cartoon_putty_scale_min, -1
set cartoon_putty_scale_max, -1
# set the B factors
alter all, b=0.2
# display the cartoons appropriately
unset cartoon_smooth_loops
unset cartoon_flat_sheets
as cartoon
cartoon putty
# unfortunately, the above does not in fact work because there is a bug in
the code when all B factors are the same...you get a radius of 1 instead.
# regardless, setting non-identical B factors should currently work:
alter chain A, b=0.2
alter chain B, b=0.4
rebuild
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:support@...
_____
From: Mark A. White [mailto:mawhite@...]
Sent: Monday, December 15, 2008 3:34 PM
To: pymol-users@...
Subject: [PyMOL] B-factor putty tube representation
Hi,
I would like to define the radius of the cartoon putty on absolute, rather
than a relative scale. Is there any way to do this? If I am comparing
rmsd, for example, I would like every image to be representative of the true
RMSD differences, rather than being a unique relative scale for each
comparison.
I notice that others have also asked about this in the past, but I did not
see a response on the Pymol-Users Email Archive. Maybe there are new
features in 1.1 that address this?
[PyMOL] putty tube representation From: Evan Kantrowitz
<evan.kantrowitz@...> - 2007-08-09 21:37
Attachments: HTML-Email.html
<http://sourceforge.net/mailarchive/attachment.php?list_name=pymol-users&mes
sage_id=5845F13B-CA26-4932-B0D2-A1131591D3EB@...&counter=1> I am
making tube representations as a comparison between two
structures. I have the rmsd in the b-factor field.
1) If I do a putty representation it works. How does the program
decide on the width variation of the tube?
2) How can this be reset?
I want to do this so when I compare two different rmsd plots the
width of lets say 1 rms is the same in both figures.
Any help would be apprecipated.
-------------------------------------------------------------------
Evan R. Kantrowitz,
Ph.D
evan.kantrowitz
Boston
College
Yours sincerely,
Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray
Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Cell. (409) 539-9138
Fax. (409) 747-4745
mailto://white@...http://xray.utmb.eduhttp://xray.utmb.edu/~white

Hi Buz,
You can use "center" as a selection name for input with zoom, along with a
distance value.
zoom center, distance
e.g.
# first, get the object you want in the center of the screen
orient
# then zoom the viewer by a fixed amount about the center point
zoom center, 10
# you may also wish to move the clipping planes in/out to avoid cutting into
any of the molecular representations:
clip atoms, 4, selection=all
# also, depending upon the application, you might want to disable
perspective
set orthoscopic
# get rid of background pixels
unset opaque_background
# render
ray
# and save
save struct001.png
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:support@...
> -----Original Message-----
> From: Buz Barstow [mailto:buzb@...]
> Sent: Monday, December 15, 2008 11:42 AM
> To: pymol-users@...
> Subject: [PyMOL] Ray Tracing A Protein Gallery
>
> Dear All,
>
> I'm making a gallery of protein molecules for my PhD thesis.
> I'd like to find an automatic way to ensure that all of the
> ray traced images have the same scale. Is there an easy way
> to do this?
>
> Thanks! and all the best,
>
> --Buz
>
> --------------------------------------------------------------
> ----------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las
> Vegas, Nevada.
> The future of the web can't happen without you. Join us at
> MIX09 to help pave the way to the Next Web now. Learn more
> and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009
.visitmix.com/
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,
I would like to define the radius of the cartoon putty on absolute,
rather than a relative scale. Is there any way to do this? If I am
comparing rmsd, for example, I would like every image to be
representative of the true RMSD differences, rather than being a unique
relative scale for each comparison.
I notice that others have also asked about this in the past, but I did
not see a response on the Pymol-Users Email Archive. Maybe there are
new features in 1.1 that address this?
[PyMOL] putty tube representation
From: Evan Kantrowitz <evan.kantrowitz@...> - 2007-08-09 21:37
Attachments: HTML-Email.html
I am making tube representations as a comparison between two
structures. I have the rmsd in the b-factor field.
1) If I do a putty representation it works. How does the program
decide on the width variation of the tube?
2) How can this be reset?
I want to do this so when I compare two different rmsd plots the
width of lets say 1 rms is the same in both figures.
Any help would be apprecipated.
-------------------------------------------------------------------
Evan R. Kantrowitz,
Ph.D
evan.kantrowitz
Boston
College
Yours sincerely,
Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics
X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Cell. (409) 539-9138
Fax. (409) 747-4745
mailto://white@...http://xray.utmb.eduhttp://xray.utmb.edu/~white

On Mon, Dec 15, 2008 at 11:41 AM, Buz Barstow <buzb@...> wrote:
> I'm making a gallery of protein molecules for my PhD thesis. I'd like
> to find an automatic way to ensure that all of the ray traced images
> have the same scale. Is there an easy way to do this?
>
Translate every model so that the center is at the origin, then use the
set_view command to apply the same viewing matrix for each model. (You can
still rotate the models, just don't zoom.) I'm not sure if there's already
a simple way to do the translation from within PyMOL, but it should be quite
straightforward using cctbx or CNS or something similar.
-Nat

Dear All,
I'm making a gallery of protein molecules for my PhD thesis. I'd like
to find an automatic way to ensure that all of the ray traced images
have the same scale. Is there an easy way to do this?
Thanks! and all the best,
--Buz